Changeset: 4b45cd344021 for MonetDB URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=4b45cd344021 Added Files: debian/monetdb-python2.install Modified Files: MonetDB.spec buildtools/ChangeLog.Dec2016 configure.ag debian/control debian/monetdb5-server.install debian/rules monetdb5/extras/rapi/rapi.R monetdb5/mal/mal_instruction.c monetdb5/optimizer/opt_wrapper.c Branch: default Log Message:
Merge. diffs (truncated from 332 to 300 lines): diff --git a/MonetDB.spec b/MonetDB.spec --- a/MonetDB.spec +++ b/MonetDB.spec @@ -88,6 +88,15 @@ %endif %if %{fedpkgs} +# If the _without_pyintegration macro is not set, the MonetDB-python2 +# RPM will be created. The macro can be set when using mock by +# passing it the flag --without=pyintegration. +%if %{?_without_pyintegration:0}%{!?_without_pyintegration:1} +%define with_pyintegration 1 +%endif +%endif + +%if %{fedpkgs} # If the _with_fits macro is set, the MonetDB-cfitsio RPM will be # created. The macro can be set when using mock by passing it the # flag --with=fits. @@ -146,7 +155,6 @@ BuildRequires: libuuid-devel BuildRequires: libxml2-devel BuildRequires: openssl-devel BuildRequires: pcre-devel >= 4.5 -BuildRequires: python-devel BuildRequires: readline-devel BuildRequires: unixODBC-devel # BuildRequires: uriparser-devel @@ -154,6 +162,10 @@ BuildRequires: zlib-devel %if %{?with_samtools:1}%{!?with_samtools:0} BuildRequires: samtools-devel %endif +%if %{?with_pyintegration:1}%{!?with_pyintegration:0} +BuildRequires: python-devel +BuildRequires: python2-numpy +%endif %if %{?with_rintegration:1}%{!?with_rintegration:0} BuildRequires: R-core-devel %endif @@ -510,6 +522,32 @@ install it. %{_libdir}/monetdb5/lib_rapi.so %endif +%if %{?with_pyintegration:1}%{!?with_pyintegration:0} +%package python2 +Summary: Integration of MonetDB and Python, allowing use of Python from within SQL +Group: Applications/Databases +Requires: MonetDB-SQL-server5%{?_isa} = %{version}-%{release} + +%description python2 +MonetDB is a database management system that is developed from a +main-memory perspective with use of a fully decomposed storage model, +automatic index management, extensibility of data types and search +accelerators. It also has an SQL frontend. + +This package contains the interface to use the Python language from +within SQL queries. This package is for Python 2. + +NOTE: INSTALLING THIS PACKAGE OPENS UP SECURITY ISSUES. If you don't +know how this package affects the security of your system, do not +install it. + +%files python2 +%defattr(-,root,root) +%{_libdir}/monetdb5/pyapi.* +%{_libdir}/monetdb5/autoload/*_pyapi.mal +%{_libdir}/monetdb5/lib_pyapi.so +%endif + %if %{?with_fits:1}%{!?with_fits:0} %package cfitsio Summary: MonetDB: Add on module that provides support for FITS files @@ -538,7 +576,6 @@ Summary: MonetDB - Monet Database Manage Group: Applications/Databases Requires(pre): shadow-utils Requires: %{name}-client%{?_isa} = %{version}-%{release} -Obsoletes: MonetDB5-server-rdf %if (0%{?fedora} >= 22) Recommends: %{name}-SQL-server5%{?_isa} = %{version}-%{release} %if %{bits} == 64 @@ -598,6 +635,9 @@ fi %if %{?with_lidar:1}%{!?with_lidar:0} %exclude %{_libdir}/monetdb5/lidar.mal %endif +%if %{?with_pyintegration:1}%{!?with_pyintegration:0} +%exclude %{_libdir}/monetdb5/pyapi.mal +%endif %if %{?with_rintegration:1}%{!?with_rintegration:0} %exclude %{_libdir}/monetdb5/rapi.mal %endif @@ -614,6 +654,9 @@ fi %if %{?with_lidar:1}%{!?with_lidar:0} %exclude %{_libdir}/monetdb5/autoload/*_lidar.mal %endif +%if %{?with_pyintegration:1}%{!?with_pyintegration:0} +%exclude %{_libdir}/monetdb5/autoload/*_pyapi.mal +%endif %if %{?with_rintegration:1}%{!?with_rintegration:0} %exclude %{_libdir}/monetdb5/autoload/*_rapi.mal %endif @@ -626,6 +669,9 @@ fi %if %{?with_lidar:1}%{!?with_lidar:0} %exclude %{_libdir}/monetdb5/lib_lidar.so %endif +%if %{?with_pyintegration:1}%{!?with_pyintegration:0} +%exclude %{_libdir}/monetdb5/lib_pyapi.so +%endif %if %{?with_rintegration:1}%{!?with_rintegration:0} %exclude %{_libdir}/monetdb5/lib_rapi.so %endif @@ -693,8 +739,6 @@ Requires: MonetDB5-server%{?_isa} = %{ve # RHEL >= 7, and all current Fedora Requires: %{_bindir}/systemd-tmpfiles %endif -Obsoletes: MonetDB-SQL-devel -Obsoletes: %{name}-SQL %if (0%{?fedora} >= 22) %if %{bits} == 64 Recommends: %{name}-SQL-server5-hugeint%{?_isa} = %{version}-%{release} @@ -785,7 +829,6 @@ frontend of MonetDB. %package testing Summary: MonetDB - Monet Database Management System Group: Applications/Databases -Obsoletes: MonetDB-python %description testing MonetDB is a database management system that is developed from a @@ -848,12 +891,12 @@ developer, but if you do want to test, t --enable-int128=%{?with_int128:yes}%{!?with_int128:no} \ --enable-lidar=%{?with_lidar:yes}%{!?with_lidar:no} \ --enable-mapi=yes \ - --enable-microhttpd=no \ --enable-monetdb5=yes \ --enable-netcdf=no \ --enable-odbc=yes \ --enable-optimize=yes \ --enable-profile=no \ + --enable-pyintegration=%{?with_pyintegration:yes}%{!?with_pyintegration:no} \ --enable-rintegration=%{?with_rintegration:yes}%{!?with_rintegration:no} \ --enable-shp=no \ --enable-sql=yes \ @@ -869,7 +912,8 @@ developer, but if you do want to test, t --with-openssl=yes \ --with-proj=no \ --with-pthread=yes \ - --with-python=yes \ + --with-python2=yes \ + --with-python3=no \ --with-readline=yes \ --with-samtools=%{?with_samtools:yes}%{!?with_samtools:no} \ --with-sphinxclient=no \ diff --git a/buildtools/ChangeLog.Dec2016 b/buildtools/ChangeLog.Dec2016 --- a/buildtools/ChangeLog.Dec2016 +++ b/buildtools/ChangeLog.Dec2016 @@ -1,6 +1,10 @@ # ChangeLog file for buildtools # This file is updated with Maddlog +* Tue Dec 6 2016 Sjoerd Mullender <sjo...@acm.org> +- New packages MonetDB-python2 (Fedora) and monetdb-python2 (Debian/Ubuntu) + have been created for Python 2 integration into MonetDB. + * Tue Jul 19 2016 Stefan Manegold <stefan.maneg...@cwi.nl> - With OID size equal to ABI/word size, mserver5 does not need to print the OID size, anymore. diff --git a/configure.ag b/configure.ag --- a/configure.ag +++ b/configure.ag @@ -1846,7 +1846,7 @@ AS_VAR_IF([enable_rintegration], [no], [ why_have_libr="(libR library not found)" enable_rintegration=no disable_rintegration="(libR library not found)"])], - [AS_IF([RHOME=`$RCMD RHOME` && libr_CFLAGS=`$RCMD CMD config --cppflags` && libr_LIBS=`$RCMD CMD config --ldflags | sed -e 's|-fopenmp |-fopenmp=libgomp'`], + [AS_IF([RHOME=`$RCMD RHOME` && libr_CFLAGS=`$RCMD CMD config --cppflags` && libr_LIBS=`$RCMD CMD config --ldflags | sed -e 's|-fopenmp |-fopenmp=libgomp |'`], [have_libr=yes AC_DEFINE([HAVE_LIBR], 1, [Define if you have libR installed]) AC_SUBST([libr_CFLAGS], [$libr_CFLAGS]) @@ -3077,7 +3077,6 @@ for comp in \ 'netcdf ' \ 'openssl ' \ 'pcre ' \ - 'perl ' \ 'proj ' \ 'pthread ' \ 'python2 ' \ diff --git a/debian/control b/debian/control --- a/debian/control +++ b/debian/control @@ -8,7 +8,7 @@ Vcs-Hg: http://dev.monetdb.org/hg/MonetD Build-Depends: debhelper (>= 5), autotools-dev, bison, libatomic-ops-dev, libbam-dev, libbz2-dev, libcurl4-gnutls-dev, libgeos-dev (>= 3.4.0), libgsl0-dev, libpcre3-dev, libreadline-dev, liblzma-dev, - libssl-dev, libxml2-dev, pkg-config, python, + libssl-dev, libxml2-dev, pkg-config, python, python-numpy, unixodbc-dev, uuid-dev, zlib1g-dev, liblas-c-dev (>= 1.8.0), r-base Standards-Version: 3.8.0 X-Python-Version: >= 2.6 @@ -272,6 +272,23 @@ Description: MonetDB5 128 bit integer (h This package provides HUGEINT (128-bit integer) support for the SQL frontend of MonetDB. +Package: monetdb-python2 +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, + monetdb5-sql (= ${source:Version}) +Description: Integration of MonetDB and Python, allowing use of Python from within SQL + MonetDB is a database management system that is developed from a + main-memory perspective with use of a fully decomposed storage model, + automatic index management, extensibility of data types and search + accelerators. It also has an SQL frontend. + . + This package contains the interface to use the Python language from + within SQL queries. This package is for Python 2. + . + NOTE: INSTALLING THIS PACKAGE OPENS UP SECURITY ISSUES. If you don't + know how this package affects the security of your system, do not + install it. + Package: monetdb-r Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, diff --git a/debian/monetdb-python2.install b/debian/monetdb-python2.install new file mode 100644 --- /dev/null +++ b/debian/monetdb-python2.install @@ -0,0 +1,3 @@ +debian/tmp/usr/lib/monetdb5/pyapi.mal usr/lib/monetdb5 +debian/tmp/usr/lib/monetdb5/autoload/??_pyapi.mal usr/lib/monetdb5/autoload +debian/tmp/usr/lib/monetdb5/lib_pyapi.so usr/lib/monetdb5 diff --git a/debian/monetdb5-server.install b/debian/monetdb5-server.install --- a/debian/monetdb5-server.install +++ b/debian/monetdb5-server.install @@ -1,26 +1,27 @@ debian/tmp/usr/bin/mserver5 usr/bin debian/tmp/usr/lib/libmonetdb5.so.* usr/lib -# usr/lib/monetdb5/lib_*.so EXCEPT: lib_{bam,geom,gsl,lidar,rapi,sql}.so +# usr/lib/monetdb5/lib_*.so EXCEPT: lib_{bam,geom,gsl,lidar,pyapi,rapi,sql}.so debian/tmp/usr/lib/monetdb5/lib_generator.so usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/lib_lsst.so usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/lib_opt_sql_append.so usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/lib_udf.so usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/lib_vault.so usr/lib/monetdb5 -# usr/lib/monetdb5/*.mal EXCEPT: {bam,geom,gsl,lidar,rapi,sql*,*_hge}.mal -debian/tmp/usr/lib/monetdb5/[!bglrsu]*.mal usr/lib/monetdb5 +# usr/lib/monetdb5/*.mal EXCEPT: {bam,geom,gsl,lidar,pyapi,rapi,sql*,*_hge}.mal +debian/tmp/usr/lib/monetdb5/[!bglprsu]*.mal usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/ba[!m]*.mal usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/b[!a]*.mal usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/generator.mal usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/g[!es]*.mal usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/l[!i]*.mal usr/lib/monetdb5 +debian/tmp/usr/lib/monetdb5/p[!y]*.mal usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/r[!a]*.mal usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/s[!q]*.mal usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/udf.mal usr/lib/monetdb5 debian/tmp/usr/lib/monetdb5/u[!d]*.mal usr/lib/monetdb5 -# usr/lib/monetdb5/autoload/*.mal EXCEPT: *_{bam,geom,gsl,hge,lidar,rapi,sql}.mal +# usr/lib/monetdb5/autoload/*.mal EXCEPT: *_{bam,geom,gsl,hge,lidar,pyapi,rapi,sql}.mal debian/tmp/usr/lib/monetdb5/autoload/??_batcalc.mal usr/lib/monetdb5/autoload debian/tmp/usr/lib/monetdb5/autoload/??_calc.mal usr/lib/monetdb5/autoload debian/tmp/usr/lib/monetdb5/autoload/??_generator.mal usr/lib/monetdb5/autoload diff --git a/debian/rules b/debian/rules --- a/debian/rules +++ b/debian/rules @@ -26,13 +26,13 @@ override_dh_auto_configure: --enable-instrument=no \ --enable-lidar=yes \ --enable-mapi=yes \ - --enable-microhttpd=no \ --enable-monetdb5=yes \ --enable-netcdf=no \ --enable-odbc=yes \ --enable-oid32=no \ --enable-optimize=yes \ --enable-profile=no \ + --enable-pyintegration=yes \ --enable-rintegration=yes \ --enable-shp=no \ --enable-sql=yes \ @@ -46,11 +46,10 @@ override_dh_auto_configure: --with-libxml2=yes \ --with-lzma=yes \ --with-openssl=yes \ - --with-perl=yes \ - --with-perl-libdir=lib/perl5 \ --with-proj=no \ --with-pthread=yes \ - --with-python=yes \ + --with-python2=yes \ + --with-python3=no \ --with-readline=yes \ --with-samtools=yes \ --with-sphinxclient=no \ diff --git a/monetdb5/extras/rapi/rapi.R b/monetdb5/extras/rapi/rapi.R --- a/monetdb5/extras/rapi/rapi.R +++ b/monetdb5/extras/rapi/rapi.R @@ -4,7 +4,7 @@ # _______________________________________________ checkin-list mailing list checkin-list@monetdb.org https://www.monetdb.org/mailman/listinfo/checkin-list